BioPy

Python bioinformatics script that is able to count nucleotides, find length of sequence, transcription DNA to RNA, reverse complement of DNA, compute GC content, count point mutations, translate RNA to protein, and find a motif in DNA. More analytical functions to be added as well as implementing FASTA format handling, and file reading. Currently runs in Python 2.7.12.

Current BioPy Functions

Note: FASTA is now accepted with the latest update. Enter a FASTA sequence into any function and works as if only a sequence was entered.

1.) Count Nucleotides in a sequence

Enter a DNA sequence and returns the number of 'A','T','C', and 'G' present. Only works for DNA currently.

Ex.) Input Sequence: ATTATTAGGGCC
     Result: Nucleotide count{'A': 3, 'C': 2, 'T': 4, 'G': 3}

2.) Transcription (DNA to RNA)

Enter a DNA sequence and converts it to RNA.

Ex.) Input Sequence: GATTCATTGGACCT
     Result: RNA: GAUUCAUUGGACCU

3.) Reverse Complement of DNA

Enter a DNA sequence and returns the reverse complement of the input.

Ex.) Input Sequence: ATTACTAGGCA
     Result: Reverse Complement: TGCCTAGTAAT

4.) FASTA Object/Handling

Enter a sequence with a FASTA format and converts the input into a FASTA object that contains
the title of the sequence, and the sequence itself. Useful for parsing data.

Ex.)

>gi|256355061:5001-2225382 Homo sapiens dystrophin (DMD), RefSeqGene (LRG_199) on chromosome X
CGTTAAATGCAAACGCTGCTCTGGCTCATGTGTTTGCTCCGAGGTATAGGTTTTGTTCGACTGACGTATC
AGATAGTCAGAGTGGTTACCACACCGACGTTGTAGCAGCTGCATAATAAATGACTGAAAGAATCATGTTA
GGCATGCCCACCTAACCTAACTTGAATCATGCGAAAGGGGAGCTGTTGGAATTCAAATAGACTTTCTGGT
TCCCAGCAGTCGGCAGTAATAGAATGCTTTCAGGAAGATGACAGAATCAGGAGAAAGATGCTGTTTTGCA
CTATCTTGATTTGTTACAGCAGCCAACTTATTGGCATGATGGAGTGACAGGAAAAACAGCTGGCATGGAA
GGTAGGATTATTAAAGCTATTACATCATTACAAATACAATTAGAAGCTGGCCATGACAAAGCATATGTTT
GAACAAGCAGCTGTTGGTAGCTGGGGTTTGTTGCCGAGCTCTTCAAACTCTGCAAACAGTGTTGCTTTTA
CAGAATGGATTTTAAAATTGCCTTGTGCTGCGTTAGATTTTGGGGAGGGGGTGTGCTTGCCTCCAACCTC

5.) Compute GC Content

Enter DNA or RNA sequence and computes how many 'G' and 'C' occur within the sequence and returns a percentage.

Ex.) Input Sequence: ATTAGCGGGGACCTGCCC
     Result: GC Content: 66.6666666667

6.) Translation (RNA to Protein)

Enter RNA sequence and the sequence is translated to protein using an amino acid table. Note that the sequence 
must contain the start codon 'AUG' somewhere in the sequence to start translation and the length from 'AUG' to
the end of the string must be divisible by three. Stopping at the stop codons or checking the reading frames has
not been implemented yet.

Ex.) Input Sequence: AAAAAUUCCGAUGGGUGAUGUUAGU
     Result: MGDVS

7.) Sequence Length

 Enter DNA, RNA, or protein sequence and returns the length of the sequence/string.
 
 Ex.) Input Sequence: ATTAGGGATGTAAAAAAAAAAA
      Result: Length of Sequence: 22 bases long.

8.) Find Motif in DNA

Enter a DNA sequence, and then enter a motif to find within that sequence. Returns locations in the sequence to 
where the motif is found.


Ex.) Input Sequence: ATTTACGACAGTTTAAAAACATCATCCCGG
     Input Motif   : CAT
     Result:       : Motif Locations: [19, 22]

9.) File Read Test

Enter a path to a text file containing a FASTA sequence or raw text sequence and BioPy will read it.

Ex.) Enter File Path: C:\Documents\Test_Files\test_sequence.txt
     Result: 
>gi|1049006351:38940602-38958746 Xenopus tropicalis strain Nigerian chromosome 9, Xenopus_tropicalis_v9.1
GCTTGTGTTTCAAATGATAAGTTCCTGGATGGCAATTAATTGCCTGTCTTGCACGACTGAGAGTCTGCAT
TTTGCCAGCTGGATGCATTGTCTGTGTGACAGCCAATCGCTGGCTCTGATGACACAAGAGAAACTCAAGT
TGGACTATAAAAGTTCACTTGGAAATAGCATGATTTATCATGGAGAGGTATTTTCTTCTTCACTTTTTAT
TTCTGTAACTGTTGGCATTACCAGAAATAGAAAATTGAATTATATGACTATATAAGAACATGAATAGGTT
ACGTGCATGGTGCTGCTGTTATCTGTGTTTGCTGGTAGCATTTAGTCCAGTGGATCTGACCAACAGCAAT
AAAGCAACAGACAAAGATACATTGTGCAGTGCCTGTACCTGGAGACAGAACAGCAAATCTTCAAGGCTTG
AAGCTATCAAACTGCAGATCCTTAGCAAACTTCGACTGGAGCAGGCACCTAATATTAGTAAGGATGCTAT
AAAATATCTTTTACCTAAAGCACCACCATTAGAAGAATTAATCGACCAGTATGACCTCCAAAGTGATGAC
AGCAGTGAGGGATCTTTGGAAGAAGATGATTACCATGCCACCACTGAAACAATCATTACAATGCCTACAG
AATGTAAGTAAAATGTTACTGTATCAAGCAGACATCTAGTTCTCATTTGGGGCACAAGTATAAATGTATT
TTTTTTTCTTTTTTCTACTGGCAAGCAGTTCGCTACTAAGCAGAAGGGTGGGGAATACAGTGACTTTTTC